Prescreening whole exome sequencing results from patients with retinal degeneration for variants in genes associated with retinal degeneration

Abstract

BackgroundAccurate clinical diagnosis and prognosis of retinal degeneration can be aided by the identification of the disease-causing genetic variant. It can confirm the clinical diagnosis as well as inform the clinician of the risk for potential involvement of other organs such as kidneys. It also aids in genetic counseling for affected individuals who want to have a child. Finally, knowledge of disease-causing variants informs laboratory investigators involved in translational research. With the advent of next-generation sequencing, identifying pathogenic mutations is becoming easier, especially the identification of novel pathogenic variants.MethodsWe used whole exome sequencing on a cohort of 69 patients with various forms of retinal degeneration and in whom screens for previously identified disease-causing variants had been inconclusive. All potential pathogenic variants were verified by Sanger sequencing and, when possible, segregation analysis of immediate relatives. Potential variants were identified by using a semi-masked approach in which rare variants in candidate genes were identified without knowledge of the clinical diagnosis (beyond “retinal degeneration”) or inheritance pattern. After the initial list of genes was prioritized, genetic diagnosis and inheritance pattern were taken into account.ResultsWe identified the likely pathogenic variants in 64% of the subjects. Seven percent had a single heterozygous mutation identified that would cause recessive disease and 13% had no obviously pathogenic variants and no family members available to perform segregation analysis. Eleven subjects are good candidates for novel gene discovery. Two de novo mutations were identified that resulted in dominant retinal degeneration.ConclusionWhole exome sequencing allows for thorough genetic analysis of candidate genes as well as novel gene discovery. It allows for an unbiased analysis of genetic variants to reduce the chance that the pathogenic mutation will be missed due to incomplete or inaccurate family history or analysis at the early stage of a syndromic form of retinal degeneration.

Mutation spectrum and clinical investigation of achromatopsia patients with mutations in the GNAT2 gene

“…In addition it is predicted to activate an exonic cryptic acceptor site. The previously reported splice site mutation c.720 + 2 T > C (Bryant, Lozynska, Maguire, Aleman, & Bennett, ) was also predicted to have a major effect on the splicing process. However, the appearance of a GC splice donor site instead of a GT splice donor site is not uncommon and holds true for approximately 1% of all splice donor sites (Burset, Seledtsov, & Solovyev, ).…”

Inherited Eye Diseases with Retinal Manifestations through the Eyes of Homeobox Genes

“…Most databases make use of Human Genome Variation Society (HGVS) nomenclature to describe variants in a consistent manner (https://varnomen.hgvs.org). To study the mechanism of variable expression, there are high hopes for genome-wide analysis techniques such as whole exome sequencing (WES) and whole genome sequencing (WGS) [327,328].…”

“…Variations in gene expression coupled with the gene's biological sources provide insight into the complex pattern of retinal gene expression that underlies specific phenotypic tissue differences, and physiologic conditions within a tissue and between normal and disease states [55]. Large-scale genetic screening of IRDs patients using whole exome/genome sequencing will continue to improve the efficiency of diagnosis through identifying novel disease-associated genes and their isoforms associated with inherited retinal degeneration [327,328].…”

“…The attitude of the International Society for Stem Cell Research (ISSCR) toward research based on the use of the listed gene technologies is ambiguous [8,351,355,356]. In parallel with the study of functions and their place in the genetic regulation program, a large-scale search for molecular targets is being carried out [327,328,394].…”

Resolving the dark matter of ABCA4 for 1,054 Stargardt disease probands through integrated genomics and transcriptomics

“…More recently, exons and splice sites have been sequenced using an amplicon tagging protocol (Zernant et al 2011;Sciezynska et al 2016), array-based hybridization (Schulz et al 2017), targeted gene-panel sequencing (Consugar et al 2015) or whole exome sequencing (Ortube et al 2014;Zhou et al 2014;Bryant et al 2018). Sequence analysis of the entire 128-kb gene and up-and downstream DNA segments was performed using next-generation sequencing platforms after enrichment of ABCA4 sequences using Raindance microdroplet-PCR target enrichment or Illumina TruSeq Custom Amplicon target enrichment (Zernant et al 2014), Haloplex-based sequence enrichment Sangermano et al 2019), or WGS (Carss et al 2017;Sangermano et al 2019).…”